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Working Backwards

What do you get when you throw anti-idiotypic antibodies into the Sargasso Sea? Well, probably not even a tiny splash, but conceptually what can be harvested is a bounty of previously undescribed and unsuspected virus genomes. When viruses infect plants, the plants fight back by generating an immune response that makes use of and is tailored to the specific virus; small RNAs, roughly 21 to 25 nucleotides in size, are synthesized by the host and used to target and destroy complementary viral RNAs. In developing a diagnostic method for two sweet potato viruses that cause corky lesions in the roots, Kreuze et al. discovered that it was possible through deep sequencing technology to recover the viral genomes by assembling the overlapping sequences of the small RNAs produced by infected plants. In addition to the expected culprits, they identified new members of the badnavirus and mastrevirus genera, which contain species that infect banana and sugarcane plants, respectively. Wu et al. have analyzed libraries of small RNA sequences derived from the fruit fly and the mosquito, and they were also able, via deep sequencing and metagenomic analysis, to identify the presence of a number of new viruses, whose complete genomes could then be reconstructed by PCR.

Meet U at the Terminal

Helen Pickersgill

Parkinson's disease is characterized by progressive neurodegeneration and has been linked to mutations in the gene parkin, which encodes a protein that recruits enzymes that catalyze the conjugation of ubiquitin to target substrates. Parkin itself contains a ubiquitin-like (Ubl) domain, which is structurally similar to ubiquitin but is not rich in proline residues. The Src homology 3 (SH3) domain is found in hundreds of copies in the human proteome, and it was originally discovered as a mediator of protein-protein interactions, particularly via its affinity for proline-rich regions. Trempe et al. have found that the Ubl domain in parkin binds to the SH3 domain in endophilin A, which is involved in the retrieval of synaptic vesicles during neuronal activity. Phosphorylation increased the interaction of parkin with endophilin A, and also stimulated the ubiquitination of a group of proteins in synaptic nerve terminals in wild-type mice, but not in parkin-deficient animals. Thus, a regulated interaction between ubiquitination and endocytosis may provide a clue to the pathophysiology in patients with Parkinson's disease.

Mol. Cell36, 1034 (2009).

Microbiology

Living Off Anesthetic

Nicholas S. Wigginton

CREDIT: JUPITERIMAGES

Toxicity concerns have largely eliminated chloroform's erstwhile use as an anesthetic, though the compound still plays a role in industrial chemistry. Low levels of chloroform (trichloromethane) inhibit the metabolisms of bacteria responsible for detoxifying many other chlorinated hydrocarbons; therefore, its persistence in the environment not only presents a possible human health risk but also slows down natural remediation processes. Now, however, Grostern et al. have discovered a population of Dehalobacter that can not only tolerate a high level of chloroform but actually grow on it by coupling dechlorination to respiration. Kinetics studies suggest that the bacteria use a reductive dehalogenase enzyme specific to chloroform and the structurally similar trichloroethane. Direct reduction of chloroform coupled to bacterial growth is advantageous for remediation because it is more efficient and does not require the addition of separate growth substrates. Contaminated aquifers—such as the one from which these bacteria were originally isolated—may be fertile grounds for other bacteria with specialized adaptations to tolerate toxins.

Environ. Microbiol.12, 10.1111/j.1462-2920.2009.02150.x (2010).

Applied Physics

Plasmons on Separate Paths

Ian S. Osborne

In the quest for faster signal processing speeds there are essentially two approaches: shrink the size of the circuitry, or use light rather than electronic current as the information carrier. In the former approach, the operating frequency faces a fundamental upper limit of several tens of GHz due to the properties of the materials required in the design of current-based devices. Light, in contrast, offers the ultimate speed, but requires circuit size to remain on the order of its roughly micrometer-scale wavelength. Surface plasmons—light-induced electronic excitations near the surface of a metal/dielectric interface—offer the possibility of exploiting the speed and size virtues of the two approaches. However, exciting the plasmons is usually a resonant phenomenon, meaning that only one kind of plasmon can be excited at a particular wavelength. Williams et al. present a technique based on a designed array of annular holes on a textured copper surface that allows two tightly bound THz-induced plasmon modes to propagate independently, thus providing potential for a number of applications in chemical and biological sensing, security screening, and communications.

Appl. Phys. Lett.96, 011101 (2010).

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